Here, we will describe the output files of many SimNIBS see File Formats in SimNIBS for a detailed description of each file type
charm generates a folder
m2m_<sub_id>/ with the segmentation results and the head mesh
<sub_id>.msh for the FEM simulations.
The final simulation results are in the Output Folder, which can be set in the GUI or in scripts. By default, this folder is called
simnibs_simulation/, and is located in the same folder as the mesh file.
Below, we have:
sub_id: Subject ID (eg. ernie)
poslist_nr: Number of simulation in poslist
cond_type: Type of conductivity used
position_nr: Coil position number.
coil_name: Name of TMS coil model.
Gmsh mesh file with tDCS simulation results
Gmsh .geo file with simplified tDCS electrode models for visualization
Gmsh mesh file with TMS simulation results
Gmsh .geo file with a simplified coil model showing it’s center and axes. For .ccd coil models, this is a more detail model showing dipoles.
Simulation configuration file, can be used to re-run the simulation
A few summary quantities for each field
In the section below, we will use
- For tDCS simulations:
- For TMS simulations:
Surface overlays with fields in the subject specific space. Generated if the Interpolate to cortical surface (GUI) or the map_to_surf (script) are set
Surface overlays with fields in FsAverage space. Generated if the Interpolate to FsAverage surface (GUI) or the map_to_fsavg (script) are set
Inside the folders, we have
Transformed result as a Gmsh .msh file for easy visualization
FreeSurfer generic overlay with given quantity (such as magn or normal) related to a given field.
NIfTI volumes with fields in a subject specific space. Generated if Interpolate to a nifiti volume (GUI) or map_to_vol (scripts) are set.
NIfTI volumes with fields in MNI space. Generated if Transform to MNI space (GUI) or map_to_mni (scripts) are set.
Inside the folders, we have NIfTI files with the field values. For vector fields such as E and J, the NIfTI files are composed of 3 volumes, each corresponding to a direction